SoroushVahidi/scidocs huggingface dataset:
The Neglected Intrinsic Resistome of Bacterial Pathogens
(2008)

Bacteria with intrinsic resistance to antibiotics are a worrisome health problem. It is widely believed that intrinsic antibiotic resistance of bacterial pathogens is mainly the consequence of cellular impermeability and activity of efflux pumps. However, the analysis of transposon-tagged Pseudomonas aeruginosa mutants presented in this article shows that this phenotype emerges from the action of numerous proteins from all functional categories. Mutations in some genes make P. aeruginosa more susceptible to antibiotics and thereby represent new targets. Mutations in other genes make P. aeruginosa more resistant and therefore define novel mechanisms for mutation-driven acquisition of antibiotic resistance, opening a new research field based in the prediction of resistance before it emerges in clinical environments. Antibiotics are not just weapons against bacterial competitors, but also natural signalling molecules. Our results demonstrate that antibiotic resistance genes are not merely protective shields and offer a more comprehensive view of the role of antibiotic resistance genes in the clinic and in nature.
Trust-Based Requirements Traceability
(2011)

Information retrieval (IR) approaches have proven useful in recovering traceability links between free-text documentation and source code. IR-based traceability recovery approaches produce ranked lists of traceability links between pieces of documentation and source code. These traceability links are then pruned using various strategies and, finally, validated by human experts. In this paper we propose two contributions to improve the precision and recall of traceability links and, thus, reduces the required human experts' manual validation effort. First, we propose a novel approach, Trust race, inspired by Web trust models to improve the precision and recall of traceability links: Trust race uses intractability recovery approach to obtain a set of traceability links, which rankings are then re-evaluated using a set of other traceability recovery approaches. Second, we propose a novel traceability recovery approach, His trace, to identify traceability links between requirements and source code through CVS/SVN change logs using a Vector Space Model (VSM). We combine a traditional recovery traceability approach with His trace to build Trust race in which we use Histraceas one expert adding knowledge to the traceability links extracttedfrom CVS/SVN  change logs. We apply Trustrace on two case studies to compare its traceability links with those recovered using only the VSM-based approach, in terms of precision and recall. We show that Trustrace improves with statistical significance the precision of the traceability links while also improving recall but without statistical significance.
A Computational Model of Graded Cueing: Robots Encouraging Behavior Change
(2013)

Our work is motivated by the evidence that children with ASD are often behind in their development of imitative behavior, and that practicing through repeated interactions with a therapist can improve imitation abilities. Our model approximates those effects with a socially assistive robot in order to use technology to broaden access to ASD therapy. Our model of graded cueing informs how specific of feedback each participant needs based on their performance in previous rounds of imitation. What is Graded Cueing? Using Probabilistic Models to Make Up for Limited Data
A Compact 27 GHz Antenna-in-Package (AiP) with RF Transmitter and Passive Phased Antenna Array
(2018)

In this paper, based on rigid-flex printed circuit board (PCB), a compact solution of Antenna-in-Package (AiP) including RF transmitter and microstrip passive phased antenna array is demonstrated. Apart from the landing of two connectors, the size shrinks down to 35 mm × 32 mm. RF transmitter works at the band of 26.2 GHz to 27.2 GHz, with conversion gain of 13 dB and rejection ratio up to 17.5 dBc. The 1 × 4 microstrip passive phased antenna array integrating 4 × 4 Butler Matrix achieves four scanning angles which are -10°, 30°, -30° and 10° with 20° half power beam width (HPBW), and simulated absolute gain is 13.51 dBi, 12.31 dBi, 12.23 dBi and 13.26 dBi respectively. Minor deviation on scanning angles from simulation data is observed in the testing due to measurement and manufacturing tolerance. However, among operating bandwidth, HPBW, main-to-side lobe ratio and the difference between two scanning angles when port 1, 4 and port 2, 3 are excited respectively are in good agreement with simulation results
5.10 A 1.4V 10.5MHz swing-boosted differential relaxation oscillator with 162.1dBc/Hz FOM and 9.86psrms period jitter in 0.18µm CMOS
(2016)

Relaxation oscillators have a profound scope as on-chip reference clock sources or sensor front-ends in comparison to ring oscillators due to their superior frequency stability, control linearity, and wide tuning range. However, despite a better fundamental limit predicted in theory, the phase noise performance of relaxation oscillators trails behind that of ring oscillators. Furthermore, there is a huge gap between the maximum achievable 1/f2 phase noise FOM (169dBc/Hz) [1] and those achieved by recently proposed low-power relaxation oscillator implementations [1-4].
Fast Text Searching Allowing Errors
(1992)

T h e string-matching problem is a very c o m m o n problem. We are searching for a string P = PtP2. . "Pro i n s i d e a la rge t ex t f i le T = t l t2. . . t . , b o t h sequences of characters from a f i n i t e character set Z. T h e characters may be English characters in a text file, DNA base pairs, lines of source code, angles between edges in polygons, machines or machine parts in a production schedule, music notes and tempo in a musical score, and so fo r th . We w a n t to f i n d a l l occurrences of P i n T; n a m e l y , we are searching for the set of starting posit ions F = {i[1 --i--n m + 1 s u c h t h a t titi+ l " " t i + m 1 = P } " T h e two most famous algorithms for this problem are t h e B o y e r M o o r e algorithm [3] and t h e K n u t h Morris Pratt algorithm [10]. There are many extensions to t h i s problem; for example, we may be looking for a set of patterns, a pattern w i t h "wi ld cards," or a regular expression. String-matching tools are included in every reasonable text editor, word processor, and many other applications.
Introduction to Automata Theory, Languages and Computation
(1979)

Let n be the pumping-lemma constant (note this n is unrelated to the n that is a local variable in the definition of the language L). Pick w = 0^n10^n. Then when we write w = xyz, we know that |xy| <= n, and therefore y consists of only 0's. Thus, xz, which must be in L if L is regular, consists of fewer than n 0's, followed by a 1 and exactly n 0's. That string is not in L, so we contradict the assumption that L is regular.
A Fast String Searching Algorithm
(1977)

An algorithm is presented that searches for the location, “<italic>i</italic>l” of the first occurrence of a character string, “<italic>pat</italic>,” in another string, “<italic>string</italic>.” During the search operation, the characters of <italic>pat</italic> are matched starting with the last character of <italic>pat</italic>. The information gained by starting the match at the end of the pattern often allows the algorithm to proceed in large jumps through the text being searched. Thus the algorithm has the unusual property that, in most cases, not all of the first <italic>i</italic> characters of <italic>string</italic> are inspected. The number of characters actually inspected (on the average) decreases as a function of the length of <italic>pat</italic>. For a random English pattern of length 5, the algorithm will typically inspect <italic>i</italic>/4 characters of <italic>string</italic> before finding a match at <italic>i</italic>. Furthermore, the algorithm has been implemented so that (on the average) fewer than <italic>i</italic> + <italic>patlen</italic> machine instructions are executed. These conclusions are supported with empirical evidence and a theoretical analysis of the average behavior of the algorithm. The worst case behavior of the algorithm is linear in <italic>i</italic> + <italic>patlen</italic>, assuming the availability of array space for tables linear in <italic>patlen</italic> plus the size of the alphabet.
3~
Black-Box Test Data Generation for GUI Testing
(2014)

Effective system testing of applications with a Graphical User Interface (GUI) front-end demands careful generation of event sequences as well as providing relevant test data for parameterized widgets, i.e., widgets that accept input values such as textboxes and textareas. Current GUI testing techniques either manipulate the source code of the application under test (AUT) to generate the test data, or blindly use a set of random string values. In this paper, we propose a third novel way to generate relevant test data for GUI testing. We exploit the information provided in the GUI structure to extract a set of key identifiers for each parameterized widget. These identifiers are used to compose appropriate search phrases and collect relevant test data from the Internet. The results of an empirical study on five GUI-based applications show that the proposed approach is applicable and can get some hard-to-cover branches in the subject programs to execute. The proposed technique works from the black-box perspective and is entirely independent from GUI modeling and event sequence generation, thus it does not need access to the source code of AUT and provides an opportunity to be integrated with the existing GUI testing frameworks.
Trend Following Trading under a Regime Switching Model
(2010)

This paper is concerned with the optimality of a trend following trading rule. The idea is to catch a bull market at its early stage, ride the trend, and liquidate the position at the first evidence of the subsequent bear market. We characterize the bull and bear phases of the markets mathematically using the conditional probabilities of the bull market given the up to date stock prices. The optimal buying and selling times are given in terms of a sequence of stopping times determined by two threshold curves. Numerical experiments are conducted to validate the theoretical results and demonstrate how they perform in a marketplace.
TASK Channels on Basal Forebrain Cholinergic Neurons Modulate Electrocortical Signatures of Arousal by Histamine.
(2015)

UNLABELLED
Basal forebrain cholinergic neurons are the main source of cortical acetylcholine, and their activation by histamine elicits cortical arousal. TWIK-like acid-sensitive K(+) (TASK) channels modulate neuronal excitability and are expressed on basal forebrain cholinergic neurons, but the role of TASK channels in the histamine-basal forebrain cholinergic arousal circuit is unknown. We first expressed TASK channel subunits and histamine Type 1 receptors in HEK cells. Application of histamine in vitro inhibited the acid-sensitive K(+) current, indicating a functionally coupled signaling mechanism. We then studied the role of TASK channels in modulating electrocortical activity in vivo using freely behaving wild-type (n = 12) and ChAT-Cre:TASK(f/f) mice (n = 12), the latter lacking TASK-1/3 channels on cholinergic neurons. TASK channel deletion on cholinergic neurons significantly altered endogenous electroencephalogram oscillations in multiple frequency bands. We then identified the effect of TASK channel deletion during microperfusion of histamine into the basal forebrain. In non-rapid eye movement sleep, TASK channel deletion on cholinergic neurons significantly attenuated the histamine-induced increase in 30-50 Hz activity, consistent with TASK channels contributing to histamine action on basal forebrain cholinergic neurons. In contrast, during active wakefulness, histamine significantly increased 30-50 Hz activity in ChAT-Cre:TASK(f/f) mice but not wild-type mice, showing that the histamine response depended upon the prevailing cortical arousal state. In summary, we identify TASK channel modulation in response to histamine receptor activation in vitro, as well as a role of TASK channels on cholinergic neurons in modulating endogenous oscillations in the electroencephalogram and the electrocortical response to histamine at the basal forebrain in vivo.


SIGNIFICANCE STATEMENT
Attentive states and cognitive function are associated with the generation of γ EEG activity. Basal forebrain cholinergic neurons are important modulators of cortical arousal and γ activity, and in this study we investigated the mechanism by which these neurons are activated by the wake-active neurotransmitter histamine. We found that histamine inhibited a class of K(+) leak channels called TASK channels and that deletion of TASK channels selectively on cholinergic neurons modulated baseline EEG activity as well as histamine-induced changes in γ activity. By identifying a discrete brain circuit where TASK channels can influence γ activity, these results represent new knowledge that enhances our understanding of how subcortical arousal systems may contribute to the generation of attentive states.
Impedance-based fault location in transmission networks: theory and application
(2014)

A number of impedance-based fault location algorithms have been developed for estimating the distance to faults in a transmission network. Each algorithm has specific input data requirements and makes certain assumptions that may or may not hold true in a particular fault location scenario. Without a detailed understanding of the principle of each fault-locating method, choosing the most suitable fault location algorithm can be a challenging task. This paper, therefore, presents the theory of one-ended (simple reactance, Takagi, modified Takagi, Eriksson, and Novosel et al.) and two-ended (synchronized, unsynchronized, and current-only) impedance-based fault location algorithms and demonstrates their application in locating real-world faults. The theory details the formulation and input data requirement of each fault-locating algorithm and evaluates the sensitivity of each to the following error sources: 1) load; 2) remote infeed; 3) fault resistance; 4) mutual coupling; 5) inaccurate line impedances; 6) DC offset and CT saturation; 7) three-terminal lines; and 8) tapped radial lines. From the theoretical analysis and field data testing, the following criteria are recommended for choosing the most suitable fault-locating algorithm: 1) data availability and 2) fault location application scenario. Another objective of this paper is to assess what additional information can be gleaned from waveforms recorded by intelligent electronic devices (IEDs) during a fault. Actual fault event data captured in utility networks is exploited to gain valuable feedback about the transmission network upstream from the IED device, and estimate the value of fault resistance.
Promoting physical activity and health literacy: study protocol for a longitudinal, mixed methods evaluation of a cross-provider workplace-related intervention in Germany (The AtRisk study)
(2016)

BACKGROUND
Physical activity and health literacy are topics of utmost importance in the prevention of chronic diseases. The present article describes the study protocol for evaluating a cross-provider workplace-related intervention promoting physical activity and health literacy.


METHODS
The RE-AIM Framework will be the conceptual framework of the AtRisk study. A controlled natural experiment and a qualitative study will be conducted. The cross-provider intervention is based on the cooperation of the German Pension Fund Rhineland and cooperating German Statutory Health Insurances. It combines two components: a behavior-oriented lifestyle intervention and the assignment of a health coach. The single-provider intervention only includes the behavior-oriented lifestyle intervention. The quantitative study (natural experiment) encompasses three measuring points (T0 = start of the behavior-oriented lifestyle intervention (baseline); T1 = end of the behavior-oriented lifestyle intervention (16 weeks); T2 = 6 month follow-up) and will compare the effectiveness of the cross-provider workplace-related intervention compared with the single provider intervention. Participants are employees with health related risk factors. ANCOVA will be used to evaluate the effect of the intervention on the outcome variables leisure time physical (primary outcome) activity and health literacy (secondary outcome). The qualitative study comprises semi-structured interviews, systematic field notes of stakeholder meetings and document analyses.


DISCUSSION
The AtRisk study will contribute towards the claim for cross-provider interventions and workplace-related approaches described in the new Preventive Health Care Act. The results of this study will inform providers, payers and policy makers about the effectiveness of a cross-provider workplace-related lifestyle intervention compared to a single-provider intervention. Beyond, the study will identify challenges for implementing cross-provider preventive interventions. With respect to the sustainability of preventive interventions the AtRisk study will give insight in the expectations and needs on health coaching from the perspective of different stakeholders.


TRIAL REGISTRATION
DRKS00010693 .
Radio resource allocation for non-orthogonal multiple access (NOMA) relay network using matching game
(2016)

In this paper, we study the resource allocation problem for a single-cell non-orthogonal multiple access (NOMA) relay network where an OFDM amplify-and-forward (AF) relay allocates the spectrum and power resources to the source-destination (SD) pairs. We aim to optimize the spectrum and power resource allocation to maximize the total sum-rate. This is a very complicated problem and the optimal approach requires an exhaustive search, leading to a NP hard problem. To solve this problem, we propose an efficient many-to-many two sided SD pair-subchannel matching algorithm in which the SD pairs and sub-channels are considered as two sets of rational and selfish players chasing their own interests. The algorithm converges to a pair-wise stable matching after a limited number of iterations with a low complexity compared with the optimal solution. Simulation results show that the sum-rate of the proposed algorithm approaches the performance of the optimal exhaustive search and significantly outperforms the conventional orthogonal multiple access scheme, in terms of the total sum-rate and number of accessed SD pairs.
CA-LSTM: Search Task Identification with Context Attention based LSTM
(2018)

Search task identification aims to understand a user's information needs to improve search quality for applications such as query suggestion, personalized search, and advertisement retrieval. To properly identify the search task within long query sessions, it is important to partition these sessions into segments before further processing. In this paper, we present the first search session segmentation model that uses a long short-term memory (LSTM) network with an attention mechanism. This model considers sequential context knowledge, including temporal information, word and character, and essentially learns which parts of the input query sequence are relevant to the current segmentation task and determines the influence of these parts. This segmentation technique is also combined with an efficient clustering method using a novel query relevance metric for end-to-end search task identification. Using real-world datasets, we demonstrate that our segmentation technique improves task identification accuracy of existing clustering-based algorithms.
StackGAN: Text to Photo-Realistic Image Synthesis with Stacked Generative Adversarial Networks
(2017)

Synthesizing high-quality images from text descriptions is a challenging problem in computer vision and has many practical applications. Samples generated by existing textto- image approaches can roughly reflect the meaning of the given descriptions, but they fail to contain necessary details and vivid object parts. In this paper, we propose Stacked Generative Adversarial Networks (StackGAN) to generate 256.256 photo-realistic images conditioned on text descriptions. We decompose the hard problem into more manageable sub-problems through a sketch-refinement process. The Stage-I GAN sketches the primitive shape and colors of the object based on the given text description, yielding Stage-I low-resolution images. The Stage-II GAN takes Stage-I results and text descriptions as inputs, and generates high-resolution images with photo-realistic details. It is able to rectify defects in Stage-I results and add compelling details with the refinement process. To improve the diversity of the synthesized images and stabilize the training of the conditional-GAN, we introduce a novel Conditioning Augmentation technique that encourages smoothness in the latent conditioning manifold. Extensive experiments and comparisons with state-of-the-arts on benchmark datasets demonstrate that the proposed method achieves significant improvements on generating photo-realistic images conditioned on text descriptions.
Digital Games in Education: The Design of Games-Based Learning Environments.
(2007)

In recentyears, electronicgames have assumed an importantplace in the lives of children and adolescents. Children acquire digital literacy informally, through plaj and neither schools nor other educational institutions take suficient account of this important aspect. We consider that multimedia design for training and education should combine the mostpowerfulfedtures of interactive multimedia design with the most effective principles of technologically-mediated learning. An examination of the evolution of the design of videogames is a good way to analyze the main contributions and characteristics ofgames-ba~edlearnin~ environments. At the same time, we will discuss the main obstacles and challenges to the use ofgames for learning. (
Efficient OFDMA for LiFi Downlink
(2018)

Light-fidelity (LiFi) relies on visible light communication to provide multiuser access in a small cell. For higher throughput, this paper studies the resource allocation problem for an orthogonal frequency-division multiplexing access scheme for LiFi downlink transmissions and presents a joint design of the bias level, power and subcarrier allocation. Decomposing the original optimization into subproblems, we first develop an efficient algorithm for the bias optimization, along with its performance analysis in terms of convergence properties and the global optimality. We then propose several power and subcarrier allocation strategies, including an optimal algorithm and a near-optimal simplified method, to satisfy different complexity and accuracy requirements. Finally, we present two algorithms to jointly optimize the bias, power, and subcarrier, and analyze the convergence properties in terms of both the objective and the solution. Comprehensive simulation results under practical LiFi system setups illustrate the effectiveness of the proposed algorithms.